It is now 2012 and I have the same question. I am not sure if I completely understand the previous response and if the suggested route was JR. We are traveling with JR Passes but if there is a shorter method (bus, local line) - I think we might be able to handle it.
Traveling from Takayama to Magome on April 5 (Thurs)
Traveling from Tsumago to Kyoto on April 8 (Sun)
This looked like I would travel to Nagoya and then take the Shinkensen to Kyoto but is that correct?
Any help or pointers greatly appreciated!